Contacts of the strand formed by residues 58 - 62 (chain A) in PDB entry 3SKU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.6 30.9 - - + +
57A VAL* 1.3 80.2 - - - +
59A TYR* 1.3 73.1 + - - +
60A ALA 4.2 0.2 - - - -
72A ASN 3.7 14.1 - - - -
73A ALA* 3.1 27.2 - - + +
74A PRO* 3.2 30.1 + - + +
177A THR* 3.6 12.6 - - + -
178A GLN 2.6 19.8 + - - +
179A PHE* 3.7 19.1 - + + -
180A ILE* 3.0 23.9 + - - +
250A SER* 4.0 17.9 - - - -
251A THR 3.3 15.3 - - - -
252A LEU* 4.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 4.4 13.3 - - + +
58A TYR* 1.3 80.4 - - - +
60A ALA* 1.3 62.7 + - - +
61A VAL* 4.2 10.2 + - + +
180A ILE* 3.3 45.2 - - + +
249A THR 4.1 0.7 - - - +
250A SER* 3.5 3.4 - - - -
251A THR* 2.9 55.6 + - + +
252A LEU* 5.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR 4.2 0.6 - - - -
59A TYR* 1.3 74.4 - - - +
61A VAL* 1.3 65.7 + - - +
69A VAL* 3.6 11.4 - - + -
70A LEU 5.2 0.2 - - - +
71A LEU* 3.5 20.8 - - + +
180A ILE 3.4 10.0 + - - +
181A LEU* 3.2 29.6 - - + -
182A GLU* 3.3 21.0 + - - +
249A THR 3.7 15.0 - - - +
250A SER* 4.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.2 13.0 + - + +
60A ALA* 1.3 82.7 - - - +
62A LEU* 1.3 57.8 + - - +
63A GLU* 3.4 16.1 + - + +
69A VAL* 5.0 2.8 - - - +
182A GLU* 3.2 30.3 - - + +
184A ARG* 4.0 28.3 - - - +
248A TYR* 3.5 22.6 - - - +
249A THR 4.5 3.8 + - - -
251A THR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 4.3 0.2 - - - -
61A VAL* 1.3 70.0 - - - +
63A GLU* 1.3 59.0 + - - +
64A ARG 3.2 23.1 - - - +
65A ALA* 3.8 18.2 - - + +
67A ARG 3.5 23.1 - - - +
69A VAL* 4.3 14.1 - - + +
156A PRO* 4.2 16.2 - - + -
181A LEU* 5.2 3.0 - - + +
182A GLU 3.0 20.6 + - - +
183A HIS* 3.2 40.8 - - + +
184A ARG* 3.1 27.7 + - - +
185A ALA* 4.2 3.8 + - + +
248A TYR* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il